diff --git a/src/Snakefiles/3-alignTips.sm b/src/Snakefiles/3-alignTips.sm
index f4e877fe..63d06941 100644
--- a/src/Snakefiles/3-alignTips.sm
+++ b/src/Snakefiles/3-alignTips.sm
@@ -120,8 +120,8 @@ cat > ./combineONT.sh <<EOF
 #!/bin/sh
 set -e
 
-cat {params.alignments} \\\\
-> ../{output.alignments}
+cat {params.alignments} | \\\\
+ sort -sk1,1 -T . > ../{output.alignments}
 
 EOF
 
diff --git a/src/scripts/select_best_alignment.py b/src/scripts/select_best_alignment.py
index b55bff8e..fd6f9e47 100755
--- a/src/scripts/select_best_alignment.py
+++ b/src/scripts/select_best_alignment.py
@@ -53,13 +53,16 @@ def mad(values, mean):
 
 		if  currID != parts[0]:
 			if len(idys) > 0:
+				assert(currID not in read_alignment_idy)
 				read_alignment_idy[currID] = [statistics.median(idys), mad(idys, statistics.mean(idys))]
 				#if len(idys) > 1: sys.stderr.write("Adding info for read %s which has mean %s and list %s and mad is %s sd %s\n"%(currID, statistics.median(idys), idys, mad(idys, statistics.mean(idys)), statistics.stdev(idys)))
 				idys.clear()
 
 		currID = parts[0]
 		idys.append(idy)
-	if len(idys) > 0: read_alignment_idy[currID] = [statistics.median(idys), mad(idys, statistics.mean(idys))]
+	if len(idys) > 0:
+		assert(currID not in read_alignment_idy)
+		read_alignment_idy[currID] = [statistics.median(idys), mad(idys, statistics.mean(idys))]
 
 # two pass, first records median alignment identity for a read, second only keeps those within some distand from median
 reads=set()